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Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing
Nicholas A Be1, James B Thissen, Shea N Gardner
1Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America.
Plos One
|September 17, 2013
Summary
Next-generation sequencing and microarrays can detect Bacillus anthracis (the cause of anthrax) in complex environmental samples. These methods offer sensitive and specific detection crucial for biodefense strategies.
Area of Science:
- Biodefense and biosurveillance
- Genomic analysis
- Microbial detection
Background:
- Bacillus anthracis causes anthrax, a significant biodefense concern.
- Detecting B. anthracis is challenging due to genomic similarity with B. cereus and B. thuringiensis.
- Sensitive and specific detection methods are vital for biodefense.
Purpose of the Study:
- To evaluate the efficacy of next-generation sequencing (NGS) and microarrays for detecting B. anthracis in environmental samples.
- To assess the sensitivity and specificity of these methods against closely related species.
Main Methods:
- Next-generation sequencing was applied to B. anthracis DNA in the presence of background nucleic acids from aerosol and soil samples.
- Reads were mapped to reference genomes and the full GenBank database for identification.
- Microbial census microarrays were also employed for B. anthracis detection.
Main Results:
- NGS detected as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid.
- Sequence data from B. anthracis was reliably distinguished from B. cereus and B. thuringiensis.
- Microarrays proved effective as a cost-effective, high-throughput complementary method.
Conclusions:
- NGS and microarrays are effective platforms for detecting B. anthracis in complex environmental backgrounds.
- These technologies are valuable components for robust biosurveillance and biodefense strategies.
- Sequencing offers additional benefits by providing genomic insights into complex or novel organisms.
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